/*
 * multi_threads.cpp
 *
 * Copyright (c) 2008-2012 BGI-Shenzhen <soap at genomics dot org dot cn>.
 *
 * This file is part of SOAPdenovo.
 *
 * SOAPdenovo is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * SOAPdenovo is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with SOAPdenovo.  If not, see <http://www.gnu.org/licenses/>.
 *
 */

#include "multi_threads.h"
#include "global.h"
#include "build_graph.h"
#include "stdinc.h"

#include "build_preArc.h"

void creatThrds ( pthread_t * threads, PARAMETER * paras )
{
	unsigned char i;
	int temp;

	for ( i = 0; i < thrd_num_s; i++ )
	{
		if ( ( temp = pthread_create ( &threads[i], NULL, threadRoutine, & ( paras[i] ) ) ) != 0 )
		{
			fprintf ( stderr, "ERROR: create threads failed.\n" );
			exit ( 1 );
		}
	}

	//fprintf(stderr,"%d work threads created.\n",thrd_num_s);
	fprintf ( stderr, "%d work threads initialized.\n", thrd_num_s );
}



void * threadRoutine ( void * para )
{
	PARAMETER * prm;
	int i;
	unsigned char id;
	prm = ( PARAMETER * ) para;
	id = prm->threadID;
	struct hashtable2 * ht = prm->ht;
	int K_size = prm->K_size;
	int gap = prm->gap;

	while ( 1 )
	{
		if ( * ( prm->selfSignal ) == 3 )
		{
			* ( prm->selfSignal ) = 0;
			break;
		}
		else if ( * ( prm->selfSignal ) == 10 )
		{
			run_process_threaded ( ht, locks, K_size, gap, read_num, thrd_num_s, prm->threadID, 1 );
			* ( prm->selfSignal ) = 0;
		}
		else if ( * ( prm->selfSignal ) == 11 )
		{
			run_process_threaded ( ht, locks, K_size, gap, read_num, thrd_num_s, prm->threadID, 2 );
			* ( prm->selfSignal ) = 0;
		}
		else if ( * ( prm->selfSignal ) == 12 )
		{
			for ( int i = prm->threadID ; i < read_num; i += thrd_num_s )
			{
				int bad_flag = 0;
				filter_N ( seq_t[i], bad_flag );

				if ( bad_flag ) {seq_t[i].clear(); continue;}

				process_1read_preArc ( prm->preArcs, locks, prm->threadID, prm->v_ht, K_size, prm->cut_off_len, seq_t[i].c_str() );
			}

			* ( prm->selfSignal ) = 0;
		}

		usleep ( 1 );
	}
}

void thread_wait ( pthread_t * threads )
{
	int i;

	for ( i = 0; i < thrd_num_s; i++ )
		if ( threads[i] != 0 )
			{ pthread_join ( threads[i], NULL ); }
}

void sendWorkSignal ( unsigned char SIG, unsigned char * thrdSignals )
{
	int t;

	for ( t = 0; t < thrd_num_s; t++ )
		{ thrdSignals[t + 1] = SIG; }

	while ( 1 )
	{
		usleep ( 10 );

		for ( t = 0; t < thrd_num_s; t++ )
			if ( thrdSignals[t + 1] )
				{ break; }

		if ( t == thrd_num_s )
			{ break; }
	}
}





















